11-791881-T-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001191061.2(SLC25A22):c.*34A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 34)
Consequence
SLC25A22
NM_001191061.2 3_prime_UTR
NM_001191061.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.47
Genes affected
SLC25A22 (HGNC:19954): (solute carrier family 25 member 22) This gene encodes a mitochondrial glutamate carrier. Mutations in this gene are associated with early infantile epileptic encephalopathy. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A22 | ENST00000628067 | c.*34A>C | 3_prime_UTR_variant | 10/10 | 1 | NM_001191061.2 | ENSP00000486058.1 | |||
SLC25A22 | ENST00000320230 | c.*34A>C | 3_prime_UTR_variant | 10/10 | 1 | ENSP00000322020.5 | ||||
SLC25A22 | ENST00000531214 | c.*34A>C | 3_prime_UTR_variant | 10/10 | 2 | ENSP00000437236.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181606Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 100854
GnomAD3 exomes
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1
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181606
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AN XY:
100854
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GnomAD4 exome Cov.: 31
GnomAD4 exome
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31
GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at